Table 1.
Characteristics of included studies (Jan 2015 to Sep 2018: n = 275)
| Study characteristic | No. of studies (Jan 2015 to Sep 2018) | ||
|---|---|---|---|
| Outbreak investigations (n = 164) | Control-oriented surveillance (n = 41) | Strategy-oriented surveillance (n = 70) | |
| Country¥,* | |||
| USA and Canada | 42 | 7 | 16 |
| UK and Ireland | 33 | 13 | 15 |
| Australia and New Zealand | 19 | 3 | 7 |
| Germany | 14 | 2 | 4 |
| Denmark | 9 | 4 | 0 |
| France | 5 | 2 | 2 |
| Setting¥ | |||
| Community | 94 | 23 | 47 |
| Institutional (hospital, school, nursery, etc.) | 73 | 21 | 25 |
| Time orientation of NGS analyses¥ | |||
| Retrospective | 97 | 18 | 59 |
| Quasi-real time | 58 | 0 | 0 |
| Prospective | 11 | 25 | 11 |
| Level of implementation of NGS analyses¥ | |||
| Proof-of-concept | 57 | 27 | 8 |
| Used to address a specific public health problem | 100 | 10 | 61 |
| Implemented into routine public health | 14 | 6 | 2 |
| Sampling fraction of NGS analyses | |||
| All available samples | 57 | 25 | 21 |
| Subset of available samples (complementary) | 107 | 16 | 48 |
| Pathogens¥ | |||
| Staphylococcus aureus | 15 | 10 | 13 |
| Multidrug-resistant Gram-negative bacteria | 27 | 4 | 12 |
| Vancomycin-resistant Enterococci (VRE) | 5 | 6 | 0 |
| Clostridium difficile | 5 | 1 | 2 |
| Streptococcus spp. | 8 | 0 | 6 |
| Listeria monocytogenes | 13 | 4 | 1 |
| Shigella spp. | 1 | 2 | 2 |
| Salmonella spp. | 33 | 5 | 8 |
| Shiga toxin-producing Escherichia coli (STEC) | 10 | 4 | 1 |
| Campylobacter jejuni | 5 | 0 | 0 |
| Legionella spp. | 10 | 0 | 1 |
| Mycobacterium spp. | 14 | 6 | 5 |
| Neisseria spp. | 6 | 0 | 14 |
| Others | 13 | 1 | 6 |
¥One study can be assigned to multiple categories
*Non-exhaustive list